I have looked into this for the company I work for, and have found it is actually done in YouTube when the video is uploaded. Almost anything can be used as a link in a video… logo to your website or Microsite, video to another video, logo to YouTube page, photo to the Flickr url… endless possibilities. Of course, you’d want to control the number of links in a video.
This is annotation is done when you upload the video to YouTube. You would then make the decision as to what is linked, to what url, and the duration, as seen in these videos below:
https://www.youtube.com/watch?v=a31wEkM6Gl8
https://youtu.be/UGeQKMJIHx8
There are a number of YouTube videos that talk about this, and give instruction.
Anna